Just after the final scene of “Before the Flood,” Sydney wakes up in the car and says Vaughn’s name before passing out again. Later, Vaughn is taken away on a stretcher as a paramedic tells someone that he’s taking care of Sydney. Before he can inject her with anything, she fights him off and escapes. Men shoot at her as she runs through a cornfield and sees Vaughn taken away in a helicopter. Back in L.A., Sydney is seen by a doctor, then gets a visit from a special investigator named Gordon Dean (Tyrees Allen). He questions her about where she and Vaughn were going (Santa Barbara) and how Vaughn was acting before the accident. Sydney doesn’t provide much information, but Dean thinks it’s because she’s being loyal to her fiancé rather than her country. Fortunately, Jack arrives to chase Dean off and make sure Sydney doesn’t say anything incriminating. He informs her that Vaughn is under investigation - Langley suspects that he’s a double agent. Elsewhere, a man greets Vaughn by calling him Mr. Michaux. As Sydney meets up with Jack and Dean at APO, Vaughn’s captor gives him a package, which contains a tape recorder that plays a song. The man pulls a piece of paper with numbers on it from one of the batteries and asks where someone named Lehman is. Vaughn says he doesn’t know who Lehman is, but the man decides to cause him some pain just to make sure.

At APO, Sydney interrupts Weiss from trying to find the helicopter to ask him why Vaughn was her handler at the CIA. Weiss says that he likes a challenge. He thinks she would be crazy to believe that Vaughn could actually be a double agent. Vaughn’s captor tries to get him to talk by pretending that Sydney is there and will be harmed. Vaughn says that the message on the paper is in code and he needs a pencil to work it out. At APO, Dean has Marshall look at Vaughn’s personal files, but Marshall thinks that he would know if Vaughn were up to anything (they “do lunch,” after all). Sydney tries to ID someone as Dixon reminds her that he gave her the benefit of the doubt when she was a double agent (see “Almost Thirty Years”), so she should do the same for Vaughn. Vaughn overpowers one of his guards and demands to know where Sydney is. The guard tells him that she escaped. Vaughn takes a page from her book and runs off. Once he’s safe, he calls her and asks her to bring him his father’s watch. After the conversation, Sydney is confronted by Jack and Dean, who have figured out that she was talking to Vaughn. Jack says that if Sydney is right and Vaughn was abducted rather than extracted by whatever organization he works for, he’s in danger. If she lets them, they can help him. Sydney tells them that Vaughn is in Mexico City.

As Vaughn goes to a locker to get the watch, Dean and some other agents set an explosion in a building in Mexico City. Both the team and Vaughn find nothing inside their respective locations. Sydney appears and offers Vaughn the watch in exchange for the truth. He tells her his real name is Andre Michaux and he’ll reveal the rest “on the way.” He continues that seven years ago he met a woman whose father was involved in a project called Prophet Five. She claimed that people were trying to cover up the project, which Vaughn’s father was also involved in. Vaughn’s first idea that the story was true came when Sydney told him about the Mueller device in “Truth Be Told” - Mueller was supposedly the head of Prophet Five. When Vaughn was 18 months old, Bill escaped from this project and changed his and his son’s identities. They’re now on their way to meet James Lehman, who worked with Bill and the woman’s father. Sydney is surprised to learn that the woman is Renee Riene. Before the conversation can continue, Sydney and Vaughn meet up with Lehman, who demands the watch. At APO, Dean tells Jack that he suspects he might know where Vaughn is. He announces that he’s naming Vaughn a fugitive and Sydney his accomplice. Marshall tells Jack that he encrypted Vaughn’s files, so Dean will never find him. Jack asks for the original files.

Lehman tells Vaughn and Sydney that a bunch of smart people were recruited in 1972 and given a page of a book called the Prophecta Chinque (the fifth prophet) to decode. The code seemed to refer to advanced genetics. Days after the code was turned in, some of the people who worked on it started to die. Bill warned Lehman about this and they both disappeared, changing their identities. Lehman knows where the book is now and he wants Vaughn to find it. Sydney and Vaughn wind up at a hotel in Cape Town, posing as a married couple. They drug someone’s drink in order to create a diversion so Vaughn can get into a safe in an office. The junction box is customized, so Sydney calls Dixon for help getting service records. While he’s waiting, Vaughn encounters a woman we’ll later know as Rachel Gibson (Rachel Nichols) and plays along with her assumption that he works with her father. While Dixon gives Sydney information, Rachel flirts with Vaughn, who isn’t having any of it. He chases her off, then opens the safe and gets the book. Rachel returns, tells him he’s fired, and presses an alarm button. As Sydney and Vaughn run off to their extraction point, Sydney gets a call from her doctor. She and Vaughn prepare to parachute off a cliff, but Sydney takes a moment to inform Vaughn that she’s pregnant.

Jack visits Sloane in his prison cell and tells him that Nadia’s condition hasn’t changed. He adds that he’s going to try to expedite Sloane’s release, but Sloane is impatient to help Nadia. Jack asks about off-book trips Vaughn took to Marseilles over the past few months; Sloane notes that the trips weren’t assignments he sent Vaughn on. Jack brings up Renee, aka the Raven, who is wanted for an assassination and the murders of three CIA agents. Her movements match up with Vaughn’s. Sloane encourages Jack to tell Sydney this. Dean talks to the woman he has attempting to decrypt Vaughn’s files; she tells him that one of Vaughn’s aliases passed through Italian customs the night before. As he leaves, we see that the woman is Rachel. Sydney and Vaughn head to a set of train tracks to meet with Lehman and Sydney asks how Vaughn feels about having a baby. He tells her that he always thought they’d wait to have children, especially considering what they do for a living, but now he can’t wait to have a baby. They joke that they’ll have to call Marshall for help with changing diapers. Lehman arrives and Vaughn crosses the tracks to give him the book. Suddenly Dean and some others arrive and start shooting. Lehman is killed and Vaughn is shot numerous times.

While Vaughn undergoes surgery, Jack chastises Sydney for putting his life in danger. He wonders why she would risk her life when she knew that he was working with Renee. Sydney tells him that she’s pregnant. As she goes to see Vaughn, Dixon calls Jack to tell him that Dean has gone off the grid and is presumed dead. Jack, Dixon, Weiss, and Marshall get to work researching Prophet Five. At the hospital, Sydney and Vaughn discuss baby names while Vaughn drinks something. Suddenly his machines start beeping and Sydney is taken out of the room. A doctor attempts to revive him but appears to be unable to. This leads to sadness and a funeral. Four months later, Sydney heads to a bar in London and meets up with Renee (Elodie Boucher). Renee doesn’t want to talk until Sydney tells her that it’s about Vaughn. Renee realizes who Sydney is and asks how she found her. Sydney says that she knows everything; Renee replies that she should have walked away. “You don’t know me very well,” Sydney replies.

WELCOME TO SPY COUNTRY: Dean, Rachel, Renee

R.I.P. (OR SO WE THINK): Vaughn

MEMORABLE QUOTES:Man: “Just tell us what we want to know. I’m tired of playing games.”
Vaughn: “Quitter.”